swash: Swash-Backwash Model for the Single Epidemic Wave

In swash: Swash-Backwash Model for the Single Epidemic Wave

Swash-Backwash Model for the Single Epidemic Wave

Description

Analysis of regional infection/surveillance data using the Swash-Backwash Model for the single epidemic wave by Cliff and Haggett (2006)

Usage

swash(
  data, 
  col_cases, 
  col_date, 
  col_region
  )

Arguments

data	data.frame with regional infection data
col_cases	Column containing the cases (numeric)
col_date	Column containing the time points (e.g., days)
col_region	Column containing the unique identifier of the regions (e.g., name, NUTS 3 code)

Details

The function performs the analysis of the input panel data using the Swash-Backwash Model. The output is an object of class "sbm". The results can be viewed using summary(sbm).

Value

object of class sbm-class

Author(s)

Thomas Wieland

References

Cliff AD, Haggett P (2006) A swash-backwash model of the single epidemic wave. Journal of Geographical Systems 8(3), 227-252. \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.1007/s10109-006-0027-8")}

Smallman-Raynor MR, Cliff AD, Stickler PJ (2022) Meningococcal Meningitis and Coal Mining in Provincial England: Geographical Perspectives on a Major Epidemic, 1929–33. Geographical Analysis 54, 197–216. \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.1111/gean.12272")}

Smallman-Raynor MR, Cliff AD, The COVID-19 Genomics UK (COG-UK) Consortium (2022) Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020–December 2021. Epidemiology and Infection 150, e145. \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.1017/S0950268822001285")}.

See Also

sbm-class

Examples

data(COVID19Cases_geoRegion)
# Get SWISS COVID19 cases at NUTS 3 level

COVID19Cases_geoRegion <- 
  COVID19Cases_geoRegion[!COVID19Cases_geoRegion$geoRegion %in% c("CH", "CHFL"),]
# Exclude CH = Switzerland total and CHFL = Switzerland and Liechtenstein total

COVID19Cases_geoRegion <- 
  COVID19Cases_geoRegion[COVID19Cases_geoRegion$datum <= "2020-05-31",]
# Extract first COVID-19 wave

CH_covidwave1 <- 
  swash (
    data = COVID19Cases_geoRegion, 
    col_cases = "entries", 
    col_date = "datum", 
    col_region = "geoRegion"
    )
# Swash-Backwash Model for Swiss COVID19 cases
# Spatial aggregate: NUTS 3 (cantons)

summary(CH_covidwave1)
# Summary of Swash-Backwash Model

plot(CH_covidwave1)
# Plot of Swash-Backwash Model edges and total epidemic curve

swash documentation built on April 12, 2025, 2:23 a.m.